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SIL file is a simple INI for with all rules of INI files apply. So when you save new information to it, the previously created enties (that were created when you saved the file with "un-excluded" properties) are still persist. So for resolving the case you would need to either:
1. Save your project translations under different file name.
2. Manually clear the file in text editor before saing translations to it.
3. Save translations to SIB file and send it to translators.